I had similar issues, along with the fees being backdated and causing even more fees. This is how they make their money. Their multimillion dollar ad campaigns for more members don't pay for themselves, you know. The fees you and I paid help fuel NFCU's growth, when they can't even support their current membership load (try going to a branch and time how long you wait in line).
Interesting that a "non-profit" entity (that you and I are part-owners of) need to assess fees like this in the first place, let alone the shifty practices of transferring funds automatically and causing the fees to occur.
I found a local credit union and haven't looked back since.